Starting phenix.real_space_refine on Thu Jul 2 03:46:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9v_37382/07_2026/8w9v_37382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9v_37382/07_2026/8w9v_37382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w9v_37382/07_2026/8w9v_37382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9v_37382/07_2026/8w9v_37382.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9v_37382/07_2026/8w9v_37382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9v_37382/07_2026/8w9v_37382.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 6 8.98 5 S 46 5.16 5 C 4324 2.51 5 N 1054 2.21 5 O 1144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6574 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3284 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain breaks: 2 Chain: "B" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3284 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' K': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' K': 3} Chain breaks: 3 Time building chain proxies: 1.76, per 1000 atoms: 0.27 Number of scatterers: 6574 At special positions: 0 Unit cell: (102.3, 86.49, 87.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 6 19.00 S 46 16.00 O 1144 8.00 N 1054 7.00 C 4324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 430.4 milliseconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 75.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 42 through 65 Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.509A pdb=" N MET A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 179 through 216 Processing helix chain 'A' and resid 216 through 227 Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 229 through 244 Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.712A pdb=" N SER A 258 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 277 through 293 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 315 through 341 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.758A pdb=" N ASP A 348 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 367 removed outlier: 3.739A pdb=" N ARG A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 429 through 445 Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'B' and resid 42 through 65 Processing helix chain 'B' and resid 75 through 88 removed outlier: 3.502A pdb=" N MET B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 115 Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 179 through 216 removed outlier: 3.527A pdb=" N HIS B 202 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Proline residue: B 222 - end of helix Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.713A pdb=" N SER B 258 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.519A pdb=" N GLN B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 293 removed outlier: 3.582A pdb=" N LEU B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 Processing helix chain 'B' and resid 315 through 341 Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.775A pdb=" N ASP B 348 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 367 removed outlier: 3.540A pdb=" N THR B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 393 Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 429 through 445 Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 479 through 485 Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 504 through 520 Processing helix chain 'B' and resid 520 through 525 449 hydrogen bonds defined for protein. 1317 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1036 1.32 - 1.45: 1764 1.45 - 1.57: 3844 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6718 Sorted by residual: bond pdb=" C ASN A 253 " pdb=" O ASN A 253 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.26e-02 6.30e+03 7.28e+00 bond pdb=" C ASN B 253 " pdb=" O ASN B 253 " ideal model delta sigma weight residual 1.235 1.211 0.024 1.26e-02 6.30e+03 3.58e+00 bond pdb=" CB PRO B 430 " pdb=" CG PRO B 430 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.16e+00 bond pdb=" N LEU A 292 " pdb=" CA LEU A 292 " ideal model delta sigma weight residual 1.460 1.474 -0.014 1.22e-02 6.72e+03 1.41e+00 bond pdb=" CA ASN A 253 " pdb=" C ASN A 253 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.34e-02 5.57e+03 1.30e+00 ... (remaining 6713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 8941 1.32 - 2.63: 138 2.63 - 3.95: 37 3.95 - 5.26: 17 5.26 - 6.58: 1 Bond angle restraints: 9134 Sorted by residual: angle pdb=" N THR B 276 " pdb=" CA THR B 276 " pdb=" C THR B 276 " ideal model delta sigma weight residual 111.14 115.20 -4.06 1.08e+00 8.57e-01 1.41e+01 angle pdb=" CA PRO B 430 " pdb=" N PRO B 430 " pdb=" CD PRO B 430 " ideal model delta sigma weight residual 112.00 108.11 3.89 1.40e+00 5.10e-01 7.70e+00 angle pdb=" C THR B 88 " pdb=" N VAL B 89 " pdb=" CA VAL B 89 " ideal model delta sigma weight residual 121.97 126.41 -4.44 1.80e+00 3.09e-01 6.07e+00 angle pdb=" O THR A 88 " pdb=" C THR A 88 " pdb=" N VAL A 89 " ideal model delta sigma weight residual 122.42 126.18 -3.76 1.61e+00 3.86e-01 5.45e+00 angle pdb=" C THR A 88 " pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta sigma weight residual 121.97 126.09 -4.12 1.80e+00 3.09e-01 5.23e+00 ... (remaining 9129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.84: 3400 13.84 - 27.68: 390 27.68 - 41.52: 107 41.52 - 55.36: 57 55.36 - 69.20: 4 Dihedral angle restraints: 3958 sinusoidal: 1500 harmonic: 2458 Sorted by residual: dihedral pdb=" CA ASN B 365 " pdb=" C ASN B 365 " pdb=" N ALA B 366 " pdb=" CA ALA B 366 " ideal model delta harmonic sigma weight residual 180.00 163.57 16.43 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA ASN B 275 " pdb=" CB ASN B 275 " pdb=" CG ASN B 275 " pdb=" OD1 ASN B 275 " ideal model delta sinusoidal sigma weight residual -90.00 -159.20 69.20 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASN A 365 " pdb=" C ASN A 365 " pdb=" N ALA A 366 " pdb=" CA ALA A 366 " ideal model delta harmonic sigma weight residual 180.00 164.64 15.36 0 5.00e+00 4.00e-02 9.43e+00 ... (remaining 3955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 945 0.052 - 0.104: 147 0.104 - 0.156: 16 0.156 - 0.208: 0 0.208 - 0.260: 2 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CA ASN A 253 " pdb=" N ASN A 253 " pdb=" C ASN A 253 " pdb=" CB ASN A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ASN B 253 " pdb=" N ASN B 253 " pdb=" C ASN B 253 " pdb=" CB ASN B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE B 374 " pdb=" N ILE B 374 " pdb=" C ILE B 374 " pdb=" CB ILE B 374 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1107 not shown) Planarity restraints: 1108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 429 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.92e+00 pdb=" N PRO B 430 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 430 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 430 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 252 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C GLU A 252 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU A 252 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 253 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 252 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C GLU B 252 " -0.027 2.00e-02 2.50e+03 pdb=" O GLU B 252 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN B 253 " 0.009 2.00e-02 2.50e+03 ... (remaining 1105 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 1912 2.81 - 3.39: 7634 3.39 - 3.98: 13246 3.98 - 4.56: 19207 4.56 - 5.14: 26759 Nonbonded interactions: 68758 Sorted by model distance: nonbonded pdb=" OE1 GLN B 424 " pdb=" OG SER B 526 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLN A 424 " pdb=" OG SER A 526 " model vdw 2.236 3.040 nonbonded pdb=" O PRO A 430 " pdb=" ND2 ASN A 434 " model vdw 2.245 3.120 nonbonded pdb=" O PHE A 361 " pdb=" ND2 ASN A 365 " model vdw 2.268 3.120 nonbonded pdb=" OH TYR B 197 " pdb=" O ALA B 273 " model vdw 2.272 3.040 ... (remaining 68753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.970 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 6718 Z= 0.135 Angle : 0.480 6.581 9134 Z= 0.253 Chirality : 0.038 0.260 1110 Planarity : 0.004 0.070 1108 Dihedral : 14.065 69.196 2370 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.93 % Allowed : 15.07 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.28), residues: 840 helix: 1.69 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -0.38 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.016 0.002 TYR A 50 PHE 0.011 0.001 PHE A 198 TRP 0.004 0.001 TRP A 45 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 6718) covalent geometry : angle 0.47964 / 0.25 ( 9134) hydrogen bonds : bond 0.15674 / 10.40 ( 449) hydrogen bonds : angle 5.39373 / 4.02 ( 1317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.254 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 87 average time/residue: 0.4870 time to fit residues: 44.8174 Evaluate side-chains 84 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 457 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 ASN A 270 GLN A 424 GLN B 253 ASN B 275 ASN B 424 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.092711 restraints weight = 8069.439| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.27 r_work: 0.2863 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6718 Z= 0.152 Angle : 0.503 5.711 9134 Z= 0.262 Chirality : 0.039 0.136 1110 Planarity : 0.005 0.049 1108 Dihedral : 4.937 54.157 904 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.47 % Allowed : 12.27 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.28), residues: 840 helix: 2.08 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.33 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 450 TYR 0.016 0.002 TYR A 50 PHE 0.012 0.001 PHE A 198 TRP 0.006 0.001 TRP B 45 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 6718) covalent geometry : angle 0.50348 / 0.26 ( 9134) hydrogen bonds : bond 0.03614 / 2.47 ( 449) hydrogen bonds : angle 4.07216 / 2.99 ( 1317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.255 Fit side-chains REVERT: A 354 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: A 434 ASN cc_start: 0.8726 (m-40) cc_final: 0.8455 (m110) REVERT: B 185 ARG cc_start: 0.6940 (mtt90) cc_final: 0.6233 (mmm-85) REVERT: B 299 ARG cc_start: 0.7367 (mtm180) cc_final: 0.6829 (mtm180) REVERT: B 434 ASN cc_start: 0.8694 (m-40) cc_final: 0.8434 (m110) outliers start: 26 outliers final: 14 residues processed: 93 average time/residue: 0.4441 time to fit residues: 43.8212 Evaluate side-chains 97 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 365 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 0.0670 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.111621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.093691 restraints weight = 8076.496| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.35 r_work: 0.2886 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6718 Z= 0.106 Angle : 0.456 5.111 9134 Z= 0.236 Chirality : 0.037 0.127 1110 Planarity : 0.004 0.047 1108 Dihedral : 4.274 46.716 898 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.07 % Allowed : 13.07 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.28), residues: 840 helix: 2.36 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.25 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 185 TYR 0.014 0.001 TYR A 50 PHE 0.011 0.001 PHE B 361 TRP 0.004 0.001 TRP B 45 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 6718) covalent geometry : angle 0.45631 / 0.24 ( 9134) hydrogen bonds : bond 0.03095 / 2.13 ( 449) hydrogen bonds : angle 3.81765 / 2.79 ( 1317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.257 Fit side-chains REVERT: A 434 ASN cc_start: 0.8755 (m-40) cc_final: 0.8505 (m110) REVERT: B 57 LEU cc_start: 0.8401 (mm) cc_final: 0.8075 (mt) REVERT: B 185 ARG cc_start: 0.7082 (mtt90) cc_final: 0.6362 (mmm-85) REVERT: B 299 ARG cc_start: 0.7473 (mtm180) cc_final: 0.7006 (mtm180) REVERT: B 434 ASN cc_start: 0.8752 (m-40) cc_final: 0.8531 (m110) REVERT: B 450 ARG cc_start: 0.7861 (ttm170) cc_final: 0.7007 (ttp-110) REVERT: B 529 LYS cc_start: 0.8507 (mttp) cc_final: 0.8278 (mmtp) outliers start: 23 outliers final: 16 residues processed: 93 average time/residue: 0.4129 time to fit residues: 40.9380 Evaluate side-chains 95 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 461 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 0.0060 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.113103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.095651 restraints weight = 8072.850| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.27 r_work: 0.2931 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6718 Z= 0.095 Angle : 0.442 5.369 9134 Z= 0.229 Chirality : 0.036 0.124 1110 Planarity : 0.004 0.048 1108 Dihedral : 4.199 46.165 898 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.33 % Allowed : 13.47 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.29), residues: 840 helix: 2.52 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -0.13 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 185 TYR 0.014 0.001 TYR A 50 PHE 0.011 0.001 PHE B 361 TRP 0.003 0.001 TRP B 287 HIS 0.002 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 6718) covalent geometry : angle 0.44234 / 0.23 ( 9134) hydrogen bonds : bond 0.02766 / 1.90 ( 449) hydrogen bonds : angle 3.65274 / 2.66 ( 1317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.241 Fit side-chains REVERT: A 434 ASN cc_start: 0.8697 (m-40) cc_final: 0.8425 (m110) REVERT: B 57 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7946 (mt) REVERT: B 185 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6310 (mmm-85) REVERT: B 299 ARG cc_start: 0.7340 (mtm180) cc_final: 0.6872 (mtm180) REVERT: B 434 ASN cc_start: 0.8703 (m-40) cc_final: 0.8491 (m110) REVERT: B 450 ARG cc_start: 0.7767 (ttm170) cc_final: 0.6880 (ttp-110) REVERT: B 461 MET cc_start: 0.8916 (mmm) cc_final: 0.8687 (OUTLIER) REVERT: B 529 LYS cc_start: 0.8473 (mttp) cc_final: 0.8236 (mmtp) outliers start: 25 outliers final: 15 residues processed: 96 average time/residue: 0.4311 time to fit residues: 44.0780 Evaluate side-chains 100 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.091659 restraints weight = 8417.145| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.36 r_work: 0.2864 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6718 Z= 0.152 Angle : 0.476 5.753 9134 Z= 0.248 Chirality : 0.038 0.135 1110 Planarity : 0.004 0.049 1108 Dihedral : 4.411 48.617 898 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.87 % Allowed : 13.47 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.28), residues: 840 helix: 2.43 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.21 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 185 TYR 0.016 0.002 TYR B 50 PHE 0.013 0.001 PHE A 198 TRP 0.004 0.001 TRP A 502 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 6718) covalent geometry : angle 0.47640 / 0.25 ( 9134) hydrogen bonds : bond 0.03147 / 2.15 ( 449) hydrogen bonds : angle 3.73115 / 2.73 ( 1317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.257 Fit side-chains REVERT: A 434 ASN cc_start: 0.8797 (m-40) cc_final: 0.8543 (m110) REVERT: B 185 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6433 (mmm-85) REVERT: B 299 ARG cc_start: 0.7381 (mtm180) cc_final: 0.6918 (mtm180) REVERT: B 434 ASN cc_start: 0.8767 (m-40) cc_final: 0.8516 (m110) REVERT: B 461 MET cc_start: 0.8998 (mmm) cc_final: 0.8790 (mmm) REVERT: B 529 LYS cc_start: 0.8542 (mttp) cc_final: 0.8308 (mmtp) outliers start: 29 outliers final: 19 residues processed: 96 average time/residue: 0.4458 time to fit residues: 45.5929 Evaluate side-chains 105 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.113185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.095781 restraints weight = 8087.894| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.26 r_work: 0.2912 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6718 Z= 0.102 Angle : 0.441 5.047 9134 Z= 0.231 Chirality : 0.037 0.125 1110 Planarity : 0.004 0.048 1108 Dihedral : 4.306 48.706 898 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.33 % Allowed : 14.00 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.29), residues: 840 helix: 2.59 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -0.17 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 185 TYR 0.013 0.001 TYR A 50 PHE 0.011 0.001 PHE A 198 TRP 0.003 0.001 TRP B 45 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 6718) covalent geometry : angle 0.44111 / 0.23 ( 9134) hydrogen bonds : bond 0.02773 / 1.90 ( 449) hydrogen bonds : angle 3.61640 / 2.64 ( 1317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.186 Fit side-chains REVERT: A 292 LEU cc_start: 0.7931 (mp) cc_final: 0.7694 (tt) REVERT: A 434 ASN cc_start: 0.8738 (m-40) cc_final: 0.8468 (m110) REVERT: B 185 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6334 (mmm-85) REVERT: B 299 ARG cc_start: 0.7337 (mtm180) cc_final: 0.6864 (mtm180) REVERT: B 434 ASN cc_start: 0.8718 (m-40) cc_final: 0.8483 (m110) REVERT: B 461 MET cc_start: 0.8942 (mmm) cc_final: 0.8736 (mmm) REVERT: B 529 LYS cc_start: 0.8499 (mttp) cc_final: 0.8269 (mmtp) outliers start: 25 outliers final: 18 residues processed: 95 average time/residue: 0.4716 time to fit residues: 47.5079 Evaluate side-chains 102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.111789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.094256 restraints weight = 8262.765| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.28 r_work: 0.2917 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6718 Z= 0.109 Angle : 0.450 6.397 9134 Z= 0.233 Chirality : 0.037 0.124 1110 Planarity : 0.004 0.048 1108 Dihedral : 4.308 49.085 898 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.07 % Allowed : 14.67 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.29), residues: 840 helix: 2.61 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 185 TYR 0.014 0.002 TYR A 50 PHE 0.011 0.001 PHE A 198 TRP 0.003 0.001 TRP A 502 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 6718) covalent geometry : angle 0.44971 / 0.23 ( 9134) hydrogen bonds : bond 0.02806 / 1.93 ( 449) hydrogen bonds : angle 3.60479 / 2.63 ( 1317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.234 Fit side-chains REVERT: A 292 LEU cc_start: 0.7941 (mp) cc_final: 0.7719 (tt) REVERT: A 434 ASN cc_start: 0.8745 (m-40) cc_final: 0.8490 (m110) REVERT: A 532 LYS cc_start: 0.7450 (mmtm) cc_final: 0.6946 (mmtp) REVERT: B 185 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6317 (mmm-85) REVERT: B 299 ARG cc_start: 0.7309 (mtm180) cc_final: 0.6834 (mtm180) REVERT: B 434 ASN cc_start: 0.8708 (m-40) cc_final: 0.8460 (m110) REVERT: B 461 MET cc_start: 0.8945 (mmm) cc_final: 0.8716 (mmm) REVERT: B 529 LYS cc_start: 0.8500 (mttp) cc_final: 0.8268 (mmtp) outliers start: 23 outliers final: 17 residues processed: 94 average time/residue: 0.4429 time to fit residues: 44.1837 Evaluate side-chains 100 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.110936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.093560 restraints weight = 8163.765| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.27 r_work: 0.2888 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6718 Z= 0.141 Angle : 0.468 5.087 9134 Z= 0.245 Chirality : 0.038 0.132 1110 Planarity : 0.004 0.049 1108 Dihedral : 4.453 50.723 898 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.07 % Allowed : 14.80 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.28), residues: 840 helix: 2.53 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -0.27 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 367 TYR 0.014 0.002 TYR A 50 PHE 0.012 0.001 PHE A 198 TRP 0.004 0.001 TRP A 502 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 6718) covalent geometry : angle 0.46829 / 0.24 ( 9134) hydrogen bonds : bond 0.03007 / 2.06 ( 449) hydrogen bonds : angle 3.66271 / 2.68 ( 1317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.180 Fit side-chains REVERT: A 292 LEU cc_start: 0.7926 (mp) cc_final: 0.7685 (tt) REVERT: A 306 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: A 434 ASN cc_start: 0.8752 (m-40) cc_final: 0.8472 (m110) REVERT: A 532 LYS cc_start: 0.7465 (mmtm) cc_final: 0.6943 (mmtp) REVERT: B 185 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6276 (mmm-85) REVERT: B 299 ARG cc_start: 0.7317 (mtm180) cc_final: 0.6834 (mtm180) REVERT: B 434 ASN cc_start: 0.8730 (m-40) cc_final: 0.8468 (m110) REVERT: B 529 LYS cc_start: 0.8523 (mttp) cc_final: 0.8285 (mmtp) outliers start: 23 outliers final: 19 residues processed: 92 average time/residue: 0.4434 time to fit residues: 43.1147 Evaluate side-chains 102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 368 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.094425 restraints weight = 8306.451| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.29 r_work: 0.2913 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6718 Z= 0.105 Angle : 0.455 6.787 9134 Z= 0.236 Chirality : 0.037 0.125 1110 Planarity : 0.004 0.048 1108 Dihedral : 4.358 50.594 898 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.40 % Allowed : 15.47 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.29), residues: 840 helix: 2.62 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -0.17 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 367 TYR 0.013 0.002 TYR A 50 PHE 0.011 0.001 PHE A 198 TRP 0.003 0.001 TRP A 502 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 6718) covalent geometry : angle 0.45474 / 0.24 ( 9134) hydrogen bonds : bond 0.02768 / 1.90 ( 449) hydrogen bonds : angle 3.59226 / 2.62 ( 1317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.173 Fit side-chains REVERT: A 306 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: A 434 ASN cc_start: 0.8752 (m-40) cc_final: 0.8474 (m110) REVERT: A 532 LYS cc_start: 0.7462 (mmtm) cc_final: 0.6937 (mmtp) REVERT: B 185 ARG cc_start: 0.7045 (mtt90) cc_final: 0.6250 (mmm-85) REVERT: B 299 ARG cc_start: 0.7283 (mtm180) cc_final: 0.6802 (mtm180) REVERT: B 375 ASP cc_start: 0.8486 (t0) cc_final: 0.8193 (t0) REVERT: B 434 ASN cc_start: 0.8720 (m-40) cc_final: 0.8467 (m110) REVERT: B 529 LYS cc_start: 0.8504 (mttp) cc_final: 0.8262 (mmtp) outliers start: 18 outliers final: 16 residues processed: 91 average time/residue: 0.4481 time to fit residues: 43.2231 Evaluate side-chains 96 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 368 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.112019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.094030 restraints weight = 8288.143| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.36 r_work: 0.2902 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6718 Z= 0.106 Angle : 0.461 9.253 9134 Z= 0.236 Chirality : 0.037 0.126 1110 Planarity : 0.004 0.048 1108 Dihedral : 4.335 50.494 898 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.27 % Allowed : 15.73 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.29), residues: 840 helix: 2.67 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -0.23 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 367 TYR 0.014 0.002 TYR A 50 PHE 0.011 0.001 PHE A 198 TRP 0.003 0.001 TRP A 502 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 6718) covalent geometry : angle 0.46120 / 0.24 ( 9134) hydrogen bonds : bond 0.02734 / 1.88 ( 449) hydrogen bonds : angle 3.55735 / 2.60 ( 1317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.237 Fit side-chains REVERT: A 299 ARG cc_start: 0.7461 (mtm180) cc_final: 0.7049 (mtm180) REVERT: A 306 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: A 434 ASN cc_start: 0.8771 (m-40) cc_final: 0.8533 (m110) REVERT: A 532 LYS cc_start: 0.7521 (mmtm) cc_final: 0.6984 (mmtp) REVERT: B 185 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6329 (mmm-85) REVERT: B 299 ARG cc_start: 0.7353 (mtm180) cc_final: 0.6878 (mtm180) REVERT: B 434 ASN cc_start: 0.8743 (m-40) cc_final: 0.8527 (m110) REVERT: B 529 LYS cc_start: 0.8512 (mttp) cc_final: 0.8273 (mmtp) outliers start: 17 outliers final: 16 residues processed: 88 average time/residue: 0.4711 time to fit residues: 43.8630 Evaluate side-chains 97 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 9.9990 chunk 36 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.112668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.095245 restraints weight = 8060.317| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.26 r_work: 0.2916 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6718 Z= 0.106 Angle : 0.455 7.081 9134 Z= 0.235 Chirality : 0.037 0.126 1110 Planarity : 0.004 0.048 1108 Dihedral : 4.331 50.445 898 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.40 % Allowed : 15.60 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.29), residues: 840 helix: 2.69 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -0.22 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 367 TYR 0.014 0.002 TYR A 50 PHE 0.011 0.001 PHE A 198 TRP 0.003 0.001 TRP A 502 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 6718) covalent geometry : angle 0.45477 / 0.24 ( 9134) hydrogen bonds : bond 0.02721 / 1.86 ( 449) hydrogen bonds : angle 3.54247 / 2.58 ( 1317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1910.83 seconds wall clock time: 33 minutes 21.79 seconds (2001.79 seconds total)